EDY81538.1 protein (Verrucomicrobiae bacterium DG1235)

Nodes:

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splice isoforms or post-translational modifications are collapsed, i.e. each node represents all the proteins produced by a single, protein-coding gene locus.

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colored nodes:
query proteins and first shell of interactors

white nodes:
second shell of interactors

Node Content

empty nodes:
proteins of unknown 3D structure

filled nodes:
a 3D structure is known or predicted

Edges:

Edges represent protein-protein associations

associations are meant to be specific and meaningful, i.e. proteins jointly contribute to a shared function; this does not necessarily mean they are physically binding to each other.

Known Interactions

from curated databases

experimentally determined

Predicted Interactions

gene neighborhood

gene fusions

gene co-occurrence

Others

textmining

co-expression

protein homology

Your Input:

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Gene Fusion

Cooccurrence

Coexpression

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[Homology]

Score

EDY81538.1

Hypothetical protein. (179 aa)

Predicted Functional Partners:

EDY82389.1

0.559

EDY81004.1

0.527

EDY83463.1

0.522

EDY81514.1

0.457

EDY83218.1

0.446

Your Current Organism:

Verrucomicrobiae bacterium DG1235

NCBI taxonomy Id: 382464
Other names: V. bacterium DG1235, Verrucomicrobiae bacterium str. DG1235, Verrucomicrobiae bacterium strain DG1235, Verrucomicrobiales bacterium DG1235

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
EDY81004.1	EDY81514.1	VDG1235_621	VDG1235_1132	TrkA-N domain family; [P] COG1226 Kef-type K+ transport systems, predicted NAD-binding component.	Hypothetical protein; [GEPR] COG0477 Permeases of the major facilitator superfamily.	0.644
EDY81004.1	EDY81538.1	VDG1235_621	VDG1235_1156	TrkA-N domain family; [P] COG1226 Kef-type K+ transport systems, predicted NAD-binding component.	Hypothetical protein.	0.527
EDY81514.1	EDY81004.1	VDG1235_1132	VDG1235_621	Hypothetical protein; [GEPR] COG0477 Permeases of the major facilitator superfamily.	TrkA-N domain family; [P] COG1226 Kef-type K+ transport systems, predicted NAD-binding component.	0.644
EDY81514.1	EDY81538.1	VDG1235_1132	VDG1235_1156	Hypothetical protein; [GEPR] COG0477 Permeases of the major facilitator superfamily.	Hypothetical protein.	0.457
EDY81538.1	EDY81004.1	VDG1235_1156	VDG1235_621	Hypothetical protein.	TrkA-N domain family; [P] COG1226 Kef-type K+ transport systems, predicted NAD-binding component.	0.527
EDY81538.1	EDY81514.1	VDG1235_1156	VDG1235_1132	Hypothetical protein.	Hypothetical protein; [GEPR] COG0477 Permeases of the major facilitator superfamily.	0.457
EDY81538.1	EDY82389.1	VDG1235_1156	VDG1235_2011	Hypothetical protein.	Hypothetical protein.	0.559
EDY81538.1	EDY83218.1	VDG1235_1156	VDG1235_2842	Hypothetical protein.	Methyltransferase domain family; [QR] COG0500 SAM-dependent methyltransferases.	0.446
EDY81538.1	EDY83463.1	VDG1235_1156	VDG1235_3090	Hypothetical protein.	Hypothetical protein.	0.522
EDY82389.1	EDY81538.1	VDG1235_2011	VDG1235_1156	Hypothetical protein.	Hypothetical protein.	0.559
EDY82389.1	EDY83218.1	VDG1235_2011	VDG1235_2842	Hypothetical protein.	Methyltransferase domain family; [QR] COG0500 SAM-dependent methyltransferases.	0.528
EDY83218.1	EDY81538.1	VDG1235_2842	VDG1235_1156	Methyltransferase domain family; [QR] COG0500 SAM-dependent methyltransferases.	Hypothetical protein.	0.446
EDY83218.1	EDY82389.1	VDG1235_2842	VDG1235_2011	Methyltransferase domain family; [QR] COG0500 SAM-dependent methyltransferases.	Hypothetical protein.	0.528
EDY83463.1	EDY81538.1	VDG1235_3090	VDG1235_1156	Hypothetical protein.	Hypothetical protein.	0.522

Network Stats

number of nodes:

11

number of edges:

22

average node degree:

4

avg. local clustering coefficient:

0.782

expected number of edges:

15

PPI enrichment p-value:

0.0566

your network does not have significantly more
interactions than expected (what does that mean?)

Functional enrichments in your networkNote: some enrichments may be expected here (why?)
disable highlight explain columns

Biological Process (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0000387

Spliceosomal snRNP assembly

4 of 19

2.36

2.57

1.18e-05

GO:0045004

DNA replication proofreading

2 of 3

2.87

1.46

0.0023

GO:0006287

Base-excision repair, gap-filling

2 of 3

2.87

1.46

0.0023

GO:0006297

Nucleotide-excision repair, DNA gap filling

2 of 5

2.64

1.38

0.0030

GO:0006289

Nucleotide-excision repair

3 of 39

1.93

1.34

0.0023

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0004536

Deoxyribonuclease activity

4 of 27

2.21

2.41

1.86e-05

GO:0003887

DNA-directed DNA polymerase activity

3 of 21

2.2

1.75

0.00045

GO:0140097

Catalytic activity, acting on DNA

5 of 159

1.54

1.61

0.00011

GO:0008296

3-5-exodeoxyribonuclease activity

2 of 8

2.44

1.18

0.0068

GO:0004520

Endodeoxyribonuclease activity

2 of 16

2.14

1.0

0.0135

(more ...)

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0043625

Delta DNA polymerase complex

3 of 4

2.92

2.62

1.64e-05

GO:0005682

U5 snRNP

3 of 12

2.44

2.26

5.65e-05

GO:0071011

Precatalytic spliceosome

3 of 15

2.34

2.23

5.65e-05

GO:0005685

U1 snRNP

3 of 15

2.34

2.23

5.65e-05

GO:0005686

U2 snRNP

3 of 18

2.26

2.19

6.17e-05

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:11192

Mixed, incl. DNA biosynthetic process, and HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA)

5 of 73

1.88

2.3

9.38e-06

CL:11298

DNA polymerase complex

3 of 11

2.48

2.24

6.24e-05

CL:6903

Spliceosomal snRNP complex, and Cleavage/polyadenylation specificity factor, A subunit, N-terminal

3 of 35

1.97

1.54

0.00090

CL:6930

mRNA splicing, and U1 snRNA binding

2 of 6

2.56

1.36

0.0032

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map03440

Homologous recombination

4 of 56

1.9

2.14

2.69e-05

map03420

Nucleotide excision repair

4 of 67

1.82

2.08

2.69e-05

map03410

Base excision repair

3 of 42

1.9

1.66

0.00040

map03430

Mismatch repair

3 of 52

1.8

1.56

0.00055

map03030

DNA replication

3 of 68

1.69

1.4

0.00095

(more ...)

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-69183

Processive synthesis on the lagging strand

3 of 31

2.03

1.34

0.0026

MAP-69166

Removal of the Flap Intermediate

3 of 29

2.06

1.34

0.0026

MAP-69186

Lagging Strand Synthesis

3 of 37

1.95

1.32

0.0026

MAP-69190

DNA strand elongation

3 of 43

1.89

1.3

0.0026

MAP-69239

Synthesis of DNA

3 of 70

1.67

1.07

0.0063

(more ...)

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0043625

Delta DNA polymerase complex

3 of 6

2.74

2.36

4.64e-05

GOCC:0034719

SMN-Sm protein complex

2 of 4

2.74

1.55

0.0015

GOCC:0000228

Nuclear chromosome

4 of 164

1.43

1.17

0.0015

GOCC:0032991

Protein-containing complex

8 of 2482

0.55

0.36

0.0278

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0239

DNA-directed DNA polymerase

2 of 6

2.56

1.25

0.0051

KW-0508

mRNA splicing

2 of 10

2.34

1.24

0.0051

KW-0004

4Fe-4S

2 of 11

2.3

1.23

0.0051

KW-0687

Ribonucleoprotein

3 of 81

1.61

1.08

0.0051

KW-0235

DNA replication

2 of 28

1.9

1.06

0.0087

(more ...)

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF14260

C4-type zinc-finger of DNA polymerase delta

2 of 2

3.04

1.28

0.0049

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR047575

Sm domain

3 of 16

2.31

1.49

0.0016

IPR001163

Sm domain, eukaryotic/archaea-type

3 of 16

2.31

1.49

0.0016

IPR010920

LSM domain superfamily

3 of 19

2.24

1.48

0.0016

IPR027248

Small nuclear ribonucleoprotein Sm D2

2 of 2

3.04

1.37

0.0034

IPR025687

C4-type zinc-finger of DNA polymerase delta

2 of 2

3.04

1.37

0.0034

(more ...)

Protein Domains (SMART)

domain

description

count in network

strength

signal

false discovery rate

SM00651

snRNP Sm proteins

3 of 13

2.4

2.1

0.00011

SM00891

ERCC4 domain

2 of 3

2.87

1.59

0.0013

SM00486

DNA polymerase type-B family

2 of 5

2.64

1.5

0.0018

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